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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for KMT2A |
 Gene summary |
| Gene information | Gene symbol | KMT2A | Gene ID | 4297 |
| Gene name | lysine methyltransferase 2A | |
| Synonyms | ALL-1|CXXC7|HRX|HTRX1|MLL|MLL1|MLL1A|TRX1|WDSTS | |
| Cytomap | 11q23.3 | |
| Type of gene | protein-coding | |
| Description | histone-lysine N-methyltransferase 2ACXXC-type zinc finger protein 7lysine (K)-specific methyltransferase 2Alysine N-methyltransferase 2Amixed lineage leukemia 1myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)trithorax-like | |
| Modification date | 20200319 | |
| UniProtAcc | A0A3B3ISN4, A0A3B3ITT0, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| KMT2A | GO:0044648 | histone H3-K4 dimethylation | 25561738 |
| KMT2A | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20861184 |
| KMT2A | GO:0051568 | histone H3-K4 methylation | 19556245 |
| KMT2A | GO:0065003 | protein-containing complex assembly | 15199122 |
| KMT2A | GO:0080182 | histone H3-K4 trimethylation | 20861184 |
| KMT2A | GO:0097692 | histone H3-K4 monomethylation | 25561738|26324722 |
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Gene structures and expression levels for KMT2A |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000118058
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| DLPFC | UP | ENST00000649699.1 | KMT2A-223:protein_coding:KMT2A | 8.412653e+01 | 1.146109e+00 | 1.130398e-04 | 7.558555e-03 |
| STG | UP | ENST00000649699.1 | KMT2A-223:protein_coding:KMT2A | 2.827902e+01 | 2.189429e+01 | 8.733443e-21 | 1.591136e-17 |
| CB | UP | ENST00000649690.1 | KMT2A-222:protein_coding:KMT2A | 3.011823e+00 | 1.051823e+00 | 6.260463e-07 | 1.007712e-05 |
| CB | UP | ENST00000533790.2 | KMT2A-211:protein_coding:KMT2A | 2.027580e+00 | 1.115170e+00 | 5.933702e-04 | 3.331729e-03 |
| CB | UP | ENST00000647944.1 | KMT2A-216:protein_coding:KMT2A | 2.718176e+00 | 1.099304e+00 | 4.508630e-03 | 1.807395e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for KMT2A |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_223323 | chr11 | 118491744:118491928:118493057:118493230:118494288:118494398 | 118493057:118493230 |
| exon_skip_225164 | chr11 | 118506546:118506646:118507508:118507609:118509136:118509200 | 118507508:118507609 |
| exon_skip_227606 | chr11 | 118481988:118482092:118482422:118482495:118484183:118484314 | 118482422:118482495 |
| exon_skip_47352 | chr11 | 118491777:118491928:118493057:118493230:118494288:118494398 | 118493057:118493230 |
| exon_skip_77931 | chr11 | 118519957:118520064:118520802:118520885:118521288:118521417 | 118520802:118520885 |
| exon_skip_95000 | chr11 | 118506546:118506646:118507529:118507609:118509136:118509200 | 118507529:118507609 |
| exon_skip_96663 | chr11 | 118484183:118484314:118484862:118484975:118488614:118488760 | 118484862:118484975 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for KMT2A |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000389506 | 118482422 | 118482495 | Frame-shift |
| ENST00000389506 | 118493057 | 118493230 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000389506 | 118482422 | 118482495 | Frame-shift |
| ENST00000389506 | 118493057 | 118493230 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000389506 | 118482422 | 118482495 | Frame-shift |
| ENST00000389506 | 118484862 | 118484975 | In-frame |
| ENST00000389506 | 118493057 | 118493230 | In-frame |
| ENST00000389506 | 118507529 | 118507609 | In-frame |
| ENST00000389506 | 118520802 | 118520885 | In-frame |
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Infer the effects of exon skipping event on protein functional features for KMT2A |
p-ENSG00000118058_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000389506 | 13672 | 3969 | 118493057 | 118493230 | 4997 | 5169 | 1665 | 1723 |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000389506 | 13672 | 3969 | 118493057 | 118493230 | 4997 | 5169 | 1665 | 1723 |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000389506 | 13672 | 3969 | 118484862 | 118484975 | 4220 | 4332 | 1406 | 1444 |
| ENST00000389506 | 13672 | 3969 | 118493057 | 118493230 | 4997 | 5169 | 1665 | 1723 |
| ENST00000389506 | 13672 | 3969 | 118507529 | 118507609 | 10747 | 10826 | 3582 | 3608 |
| ENST00000389506 | 13672 | 3969 | 118520802 | 118520885 | 11422 | 11504 | 3807 | 3834 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q03164 | 1665 | 1723 | 1 | 3969 | Chain | ID=PRO_0000124876;Note=Histone-lysine N-methyltransferase 2A |
| Q03164 | 1665 | 1723 | 1 | 2718 | Chain | ID=PRO_0000390949;Note=MLL cleavage product N320 |
| Q03164 | 1665 | 1723 | 1703 | 1748 | Domain | Note=Bromo%3B divergent;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q03164 | 1665 | 1723 | 1708 | 1716 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LQH |
| Q03164 | 1665 | 1723 | 1723 | 1740 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LQH |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q03164 | 1665 | 1723 | 1 | 3969 | Chain | ID=PRO_0000124876;Note=Histone-lysine N-methyltransferase 2A |
| Q03164 | 1665 | 1723 | 1 | 2718 | Chain | ID=PRO_0000390949;Note=MLL cleavage product N320 |
| Q03164 | 1665 | 1723 | 1703 | 1748 | Domain | Note=Bromo%3B divergent;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q03164 | 1665 | 1723 | 1708 | 1716 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LQH |
| Q03164 | 1665 | 1723 | 1723 | 1740 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LQH |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q03164 | 1406 | 1444 | 1407 | 1444 | Alternative sequence | ID=VSP_006666;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7598802;Dbxref=PMID:7598802 |
| Q03164 | 1406 | 1444 | 1 | 3969 | Chain | ID=PRO_0000124876;Note=Histone-lysine N-methyltransferase 2A |
| Q03164 | 1406 | 1444 | 1 | 2718 | Chain | ID=PRO_0000390949;Note=MLL cleavage product N320 |
| Q03164 | 1406 | 1444 | 1406 | 1407 | Site | Note=Breakpoint for translocation to form KMT2A-AFF4 fusion protein |
| Q03164 | 1406 | 1444 | 1444 | 1445 | Site | Note=Breakpoint for translocation to form KMT2A-GAS7 oncogene |
| Q03164 | 1406 | 1444 | 1444 | 1445 | Site | Note=Breakpoint for translocation to form KMT2A-LPP |
| Q03164 | 1406 | 1444 | 1431 | 1482 | Zinc finger | Note=PHD-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00146 |
| Q03164 | 1665 | 1723 | 1 | 3969 | Chain | ID=PRO_0000124876;Note=Histone-lysine N-methyltransferase 2A |
| Q03164 | 1665 | 1723 | 1 | 2718 | Chain | ID=PRO_0000390949;Note=MLL cleavage product N320 |
| Q03164 | 1665 | 1723 | 1703 | 1748 | Domain | Note=Bromo%3B divergent;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00035 |
| Q03164 | 1665 | 1723 | 1708 | 1716 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LQH |
| Q03164 | 1665 | 1723 | 1723 | 1740 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LQH |
| Q03164 | 3582 | 3608 | 1 | 3969 | Chain | ID=PRO_0000124876;Note=Histone-lysine N-methyltransferase 2A |
| Q03164 | 3582 | 3608 | 2719 | 3969 | Chain | ID=PRO_0000390950;Note=MLL cleavage product C180 |
| Q03164 | 3807 | 3834 | 3831 | 3835 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F5E |
| Q03164 | 3807 | 3834 | 1 | 3969 | Chain | ID=PRO_0000124876;Note=Histone-lysine N-methyltransferase 2A |
| Q03164 | 3807 | 3834 | 2719 | 3969 | Chain | ID=PRO_0000390950;Note=MLL cleavage product C180 |
| Q03164 | 3807 | 3834 | 3829 | 3945 | Domain | Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00190 |
| Q03164 | 3807 | 3834 | 3809 | 3811 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2W5Y |
| Q03164 | 3807 | 3834 | 3816 | 3820 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F5E |
| Q03164 | 3807 | 3834 | 3823 | 3830 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5F5E |
| Q03164 | 3807 | 3834 | 3813 | 3813 | Sequence conflict | Note=D->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in KMT2A |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for KMT2A |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for KMT2A |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KMT2A |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for KMT2A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for KMT2A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for KMT2A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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